If you wish to dye your fondant, it is easiest to use a food processor. Break up the chunk of fondant you wish to dye into four or five pieces and put in the food processor with the desired amount of colouring.
When you turn on the blades the fondant will break apart into tiny pieces right away, eventually collecting back together to form one large marbled lump. At this point you can remove the mass and finish kneading the colour through by hand.
Making sure your hands are well greased with shortening with help repel fondant and dye.